Details of CH4114 (Autumn 2025)
Level: 4 | Type: Theory | Credits: 4.0 |
Course Code | Course Name | Instructor(s) |
---|---|---|
CH4114 | Molecular Simulation | Neelanjana Sengupta, Susmita Roy |
Preamble |
---|
Preamble: This course will introduce concepts and methods underlying molecular dynamics
simulations of multi-component (bio)molecular systems. It should equip one with skills for designing meaningful simulations, data analysis and benchmarking with experimental observations. The course will involve a simulation project in the latter half (*). * The total number of participants will be limited. |
Syllabus |
---|
1. Introduction to Molecular Simulations
a. History of development b. Bottoms-up approach: the Computational Microscope 2. Statistical mechanics background a. Microscopic and macroscopic parameters b. Phase space and Ensembles c. Equilibrium and ergodicity 3. The MD engine a. Empirical potentials: the Force Field b. Many-body equations of motion; numerical solutions c. Thermodynamic control: thermostats and barostats d. Periodic boundary conditions; attaining the thermodynamic limit 4. Standard analysis toolbox a. Static vs. dynamic quantities b. Structural analysis 5. Transitions in free energy landscapes a. Local and global minima; transition states b. Collective variables; enhanced sampling 6. Project: a. System setup and simulation b. Identification of equilibrium c. Data analysis |
Prerequisite |
---|
Basic understanding of thermodynamics and biomolecular structure. Working knowledge of Linux
Suitability: Senior BS-MS students; IPhD students; Research Scholar from both DCS and DBS |
References |
---|
References:
1. Computer Simulations of Liquids, M.P Allen and D.J Tildesley (Oxford) 2. Understanding Molecular Simulation: D. Frenkel and B. Smit (Elsevier) 3. The Art of Molecular Dynamics Simulations: D. C. Rapaport (Cambridge) 4. Additional material will be provided |
Course Credit Options
Sl. No. | Programme | Semester No | Course Choice |
---|---|---|---|
1 | IP | 1 | Not Allowed |
2 | IP | 3 | Not Allowed |
3 | IP | 5 | Not Allowed |
4 | MP | 1 | Not Allowed |
5 | MP | 3 | Elective |
6 | MR | 1 | Not Allowed |
7 | MR | 3 | Not Allowed |
8 | MS | 3 | Not Allowed |
9 | MS | 5 | Not Allowed |
10 | MS | 7 | Elective |
11 | MS | 9 | Elective |
12 | RS | 1 | Elective |
13 | RS | 2 | Elective |